The genome-wide landscape of small insertion and deletion mutations in Monopterus albus

Feng Chen; Fengling Lai; Majing Luo; Yu-San Han; Hanhua Cheng; Rongjia Zhou

doi:10.1016/j.jgg.2019.02.002

Volume 46 Issue 2

Feb. 2019

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Article Navigation > Journal of Genetics and Genomics > 2019 > 46(2): 75-86

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The genome-wide landscape of small insertion and deletion mutations in Monopterus albus

doi: 10.1016/j.jgg.2019.02.002

a
Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
b
Institute of Fisheries Science, College of Life Science, "National Taiwan University", Taipei, 10617, Taiwan, China

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Corresponding author: E-mail address: hhcheng@whu.edu.cn (Hanhua Cheng); E-mail address: rjzhou@whu.edu.cn (Rongjia Zhou)
Received Date: 2018-09-30
Accepted Date: 2019-02-01
Rev Recd Date: 2018-12-21

Available Online: 2019-02-23

Publish Date: 2019-02-01

Abstract

Abstract

Insertion and deletion (indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels inMonopterus population. Over 2000 indels in 1738 indel genes, including 1–21 bp deletions and 1–15 bp insertions, were detected. Each indel gene had ∼1.1 deletions/insertions, and 2–4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to non-indel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.
- Sex determination,
- Insertions,
- Deletions,
- Evolution,
- Reproduction

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